If they think the "Beast from the East". is bad then they should wait till HS2 becomes operational. When the rail journey time is 3 hours or less, people tend to prefer the train, indeed Eurostar took a huge share of the London-Paris/Brussels air travel market. If the new Azumas on the East Coast are cleared for 140mph running (and the conventional signalling in place is designed to enable that), then anything London-Leeds/Newcastle/Edinburgh will lose out to rail.
A lot of domestic air travel will be hit but the other operators are much less dependent on domestic routes.
Personally, unless Flybe adopts a change of strategy to avoid competing with rail, I think they'll really struggle in the long-term.